Care to make some names, with their reason following?
Anhalt, Ansbach, Baden, Bremen, Brunswick, Frankfurt, Hamburg, Hannover, Hessen, Kleves, Cologne, Lorraine, Luneburg, Magdeburg, Mainz, Meissen, Munster, Oldenburg, Palatinate, Pommerania, Saxony, Silesia, Salzburg, Styria, Thuringia, Tirol, Trier, Wurzburg, Westfalia, Wurttemberg.
Reasoning? They're minors that historically did nothing, individually, until bigger states absorbed them. You talk about SimCity in an EU3 setting: many of these statelets are literally that. A case can certainly be made for Austria or Prussia (or Venice or Milan) being countries with interesting military and diplomatic histories, but these? You think they are interesting: you tell me why.
Thinking about the importance of nations throughout the world in 1900-2000 is one thing, but between 1700 and 1800, outside Europe...actually who and why?
The game starts in 1399, not 1700. I either lose in the first 30 years or have won by 1550. So I think the period from 1400 to 1550 is as relevant as 1700 to 1800. During that time significant/important/interesting countries outside Europe include the Ottomans (not sure whether they'd be considered "outside Europe"), the Mamlukes, the Saffavids, the Timurids and Moghuls, the Delhi Sultanate, the Bahmanids and Vijayanagar, Ming, Japan, the Aztecs, the Incas, Songhai. EU3 is mostly about warfare and diplomacy and all of these countries had much more interesting military histories than any of those HRE statelets. If you want to play a trading game, any of the Swahili city-states or Gujarat or Oman are comparable to the German city-states. Later states would include the Marathas and Sikhs in India and the Jurchens in China. (Why is Jurchen->Manchu->Qing less interesting than TO->Prussia->Germany?)
The Inca are 'potentially interesting'?
Again, you declare a fault but you do not tell why, and what should be done to improve it.
You took a good example however...just how can be a game be fun playing a nation surrounded by savage lands, with your own men even lacking horses, nothing particular about historical events or historical innovations?
Historically, the Incas were a one-province minor in 1400. They stayed that way until about 1428, at which point they started expanding, rapidly. So that already suggests that an Incas game would start by working towards something, a decision or mission or national idea, lots of different mechanics are possible, which would give them the ability to expand into neighbouring provinces. Then the player would have strategic decisions to make: how far to expand, how fast? Historically the Incas were influenced in their form of government by the Chimu. The player could decide whether to follow history there or not. Then there would come a "smallpox" event: ruler dies, heir dies, provinces lose tax base and population, stability way down, civil war, revolts all over the place (the "Inca Empire" was not, historically, ethnically homogenous). Can you, the player, recover from that well enough to face off the Europeans when they show up? If you do, should you convert to Christianity? Kongo did: it's not impossible. (Similarly the Funj converted to Islam and the Oirat converted to Buddhism.) But it would be hard for a country whose government and religion were as intertwined as the Incas.
They start without horses? There's another goal for the player to work towards: some set of criteria at which point the country gets access to cavalry by mission or decision or event.
Historically most of the African nations (11 out of 16) in the game had cavalry. It's only in the game that they don't. Yes, not giving cavalry to countries that historically had cavalry makes the game less interesting.
The Aztecs? Being isolated with only two neighbours is obviously not particularly interesting. Especially when simply moving into a province allows you to instantly conquer it, and the AI is moving its main army as if you were in Europe with forts in every province. But "Zapotec" and "Maya" as they exist in game did not exist: the area consisted of a lot of small states. So a lot of diplomacy would be possible. And historically simply moving an army into an area was not enough to take it: you had to spend a fair amount of time establishing control. There were local armies better represented by forts than by conventional troops. So conquering your neighbours as the Aztecs should be less trivial than the current game of "Risk".
Or consider North America. In game, whoever lands on the east coast first insta-conquers the 5 native states there and by maybe 1550 European civilization has advanced to the Mississippi, which historically took until the early 1800's. In real history, establishing the first colonies was difficult. Then the French allied with the Hurons and the English with the Iroquois. But in game European countries can't ally with the Hurons or Iroquois without vassalizing them: it's hard-coded because they're a different religion group. I'd say the historical developments are more interesting than what happens in game.
Some of these suggestions I'm making are hard, which is why I'm posting in a thread about expansions, but some are very very easy. Exactly how would it make the game worse for people playing European countries if the Aztecs could send merchants to the CoT in Mexico city?